// get_arg.h
//

#if !defined(GETARG_H)
#define GETARG_H

#if _MSC_VER > 1000
#pragma once
#endif // _MSC_VER > 1000

#include <string>
//#include <iosfwd>
#include <fstream>
#include <boost/shared_ptr.hpp>


enum eREGION {eMASKED = 1, eINVERSE = 2, eWHOLE = 4};
class t_program_args
{
public:
	
	// for error / progress messages etc.
	std::string		paml;
    std::string		output_prefix;
	std::string		error_file;
	std::string		tempdir;
	bool			codeml;
	bool			fixed_kappa;
	double			kappa;



	// for initializing this struct
	friend
	bool process_command_line_options(int argc, char* argv[], t_program_args& args);
};

bool process_command_line_options(int argc, char* argv[], t_program_args& args);
#endif //GETARG_H

